Putnam was elected president of the American Library Association in 1898 and again in 1904, and was appointed Librarian of Congress in 1899 by President William McKinley. He was the first experienced librarian to hold the post. He held the post until 1939 when he retired with the title of librarian emeritus to be succeeded by the poet Archibald MacLeish. Early during his administration, Putnam introduced a new system of classifying books that continues to this day as the Library of Congress classification. He also established an interlibrary loan system, and expanded the Library of Congress's role and relationships with other libraries, through the provision of centralized services.